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- PDB-6cpr: Crystal structure of 4-1BBL/4-1BB complex in C2 space group -

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Basic information

Entry
Database: PDB / ID: 6cpr
TitleCrystal structure of 4-1BBL/4-1BB complex in C2 space group
Components(Tumor necrosis factor ...) x 2
KeywordsCYTOKINE / complex
Function / homology
Function and homology information


tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / tumor necrosis factor receptor binding / regulation of T cell proliferation / positive regulation of activated T cell proliferation / cytokine activity / cell-cell signaling / signaling receptor activity ...tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / tumor necrosis factor receptor binding / regulation of T cell proliferation / positive regulation of activated T cell proliferation / cytokine activity / cell-cell signaling / signaling receptor activity / regulation of cell population proliferation / regulation of apoptotic process / immune response / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / apoptotic process / extracellular space / plasma membrane
Similarity search - Function
Tumor necrosis factor ligand superfamily member 9 / Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / Tumor necrosis factor (TNF) homology domain (THD) profile. / TNF(Tumour Necrosis Factor) family ...Tumor necrosis factor ligand superfamily member 9 / Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / Tumor necrosis factor (TNF) homology domain (THD) profile. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Growth factor receptor cysteine-rich domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 9 / Tumor necrosis factor receptor superfamily member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAruna, B. / Zajonc, D.M.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Crystal structures of the human 4-1BB receptor bound to its ligand 4-1BBL reveal covalent receptor dimerization as a potential signaling amplifier.
Authors: Bitra, A. / Doukov, T. / Croft, M. / Zajonc, D.M.
History
DepositionMar 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor ligand superfamily member 9
B: Tumor necrosis factor ligand superfamily member 9
C: Tumor necrosis factor ligand superfamily member 9
D: Tumor necrosis factor receptor superfamily member 9
F: Tumor necrosis factor receptor superfamily member 9
E: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,76925
Polymers97,1426
Non-polymers1,62619
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.280, 66.504, 129.356
Angle α, β, γ (deg.)90.000, 103.090, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C
14D
24F
15D
25E
16F
26E

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA90 - 24211 - 163
21GLYGLYPROPROBB90 - 24211 - 163
12GLYGLYVALVALAA90 - 24011 - 161
22GLYGLYVALVALCC90 - 24011 - 161
13GLYGLYVALVALBB90 - 24011 - 161
23GLYGLYVALVALCC90 - 24011 - 161
14PROPROVALVALDD27 - 1575 - 135
24PROPROVALVALFE27 - 1575 - 135
15PROPROCYSCYSDD27 - 1585 - 136
25PROPROCYSCYSEF27 - 1585 - 136
16ASPASPVALVALFE26 - 1574 - 135
26ASPASPVALVALEF26 - 1574 - 135

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.499954, -0.866048, -0.002489), (0.86605, -0.499956, 0.000445), (-0.00163, -0.001933, 0.999997)63.26992, -39.639462, 0.11075

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Components

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Tumor necrosis factor ... , 2 types, 6 molecules ABCDFE

#1: Protein Tumor necrosis factor ligand superfamily member 9 / 4-1BB ligand / 4-1BBL


Mass: 17488.945 Da / Num. of mol.: 3 / Fragment: residues 80-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF9
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P41273
#2: Protein Tumor necrosis factor receptor superfamily member 9 / 4-1BB ligand receptor / CDw137 / T-cell antigen 4-1BB homolog / T-cell antigen ILA


Mass: 14891.838 Da / Num. of mol.: 3 / Fragment: residues 23-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF9, CD137, ILA
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q07011

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Sugars , 1 types, 3 molecules

#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 164 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na acetate pH 4.6 10% W/V PEG 4000 0.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→38 Å / Num. obs: 25892 / % possible obs: 97.7 % / Redundancy: 5.744 % / Biso Wilson estimate: 61.482 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.143 / Rrim(I) all: 0.156 / Χ2: 0.973 / Net I/σ(I): 7.8 / Num. measured all: 148726 / Scaling rejects: 362
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.775.0160.9211.959501198518940.8171.02295.4
2.77-2.855.2250.7952.359284183917770.8410.8896.6
2.85-2.935.8650.5883.2910797186418410.8810.64398.8
2.93-3.025.8480.4544.2210514180917980.920.49799.4
3.02-3.125.9540.4034.519985169816770.9430.4498.8
3.12-3.235.9480.3495.289690167216290.9510.38297.4
3.23-3.355.9260.2676.289446163815940.9690.29297.3
3.35-3.495.420.227.048304159215320.9730.24296.2
3.49-3.646.0640.1848.48854147714600.9850.20198.8
3.64-3.826.1630.1469.868801145514280.9860.1698.1
3.82-4.035.9940.1410.657906134313190.9860.15298.2
4.03-4.275.910.11711.67541129812760.9910.12898.3
4.27-4.565.3710.10412.196268121311670.990.11496.2
4.56-4.9360.112.936852115411420.9930.10999
4.93-5.46.0630.09813.716275104410350.9930.10699.1
5.4-6.045.8930.10212.9956639849610.990.11197.7
6.04-6.975.2950.10811.4740778137700.9930.1294.7
6.97-8.545.8580.09513.4642417287240.9930.10499.5
8.54-12.085.5110.09315.5230865665600.9930.10198.9
12.08-385.3280.07817.6316413293080.9940.08593.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X29, 5WI8

2x29

5wi8


Resolution: 2.7→38 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.901 / SU B: 18.138 / SU ML: 0.357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2796 1320 5.1 %RANDOM
Rwork0.2487 ---
obs0.2503 24498 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.84 Å2 / Biso mean: 61.638 Å2 / Biso min: 26.05 Å2
Baniso -1Baniso -2Baniso -3
1--4.38 Å20 Å21.91 Å2
2---3.1 Å20 Å2
3---5.95 Å2
Refinement stepCycle: final / Resolution: 2.7→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6022 0 87 148 6257
Biso mean--102 53.72 -
Num. residues----848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196252
X-RAY DIFFRACTIONr_bond_other_d0.0020.025412
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.968514
X-RAY DIFFRACTIONr_angle_other_deg0.942312505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0945837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95123.745235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24915858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7761536
X-RAY DIFFRACTIONr_chiral_restr0.0770.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217137
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021264
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1263MEDIUM POSITIONAL0.010.5
1A883TIGHT THERMAL3.590.5
1A1263MEDIUM THERMAL3.992
2A1223MEDIUM POSITIONAL0.010.5
2A861TIGHT THERMAL3.40.5
2A1223MEDIUM THERMAL3.362
3B1255MEDIUM POSITIONAL0.010.5
3B855TIGHT THERMAL3.740.5
3B1255MEDIUM THERMAL3.862
4D788MEDIUM POSITIONAL0.020.5
4D754TIGHT THERMAL4.080.5
4D788MEDIUM THERMAL4.72
5D813MEDIUM POSITIONAL0.020.5
5D760TIGHT THERMAL4.560.5
5D813MEDIUM THERMAL4.422
6F795MEDIUM POSITIONAL0.020.5
6F760TIGHT THERMAL4.580.5
6F795MEDIUM THERMAL4.792
LS refinement shellResolution: 2.701→2.771 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 85 -
Rwork0.392 1729 -
all-1814 -
obs--91.85 %

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